Add filter_leading_zeros and zero_threshold to estimate_secondary() and estimate_truncation()
#608
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jamesmbaazam
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Co-authored-by: Sebastian Funk <[email protected]>
Co-authored-by: Sebastian Funk <[email protected]>
Co-authored-by: Sebastian Funk <[email protected]>
Co-authored-by: Sebastian Funk <[email protected]>
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sbfnk
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This looks good now. I can make the minor changes needed to fix the tests and then, once you @jamesmbaazam approve, we can merge. |
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I can't approve because I'm the last pusher. |
seabbs
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…y()` and `estimate_truncation()` (#608) * Add filter_leading_zeros and zero_threshold to estimate_secondary() * Add filter_leading_zeros and zero_threshold to estimate_truncation() * Call create_clean_reported_cases() in estimate_truncation() * Remove breakpoint column created by create_clean_reported_cases() * Add tests for the new arguments * Fix wrong object name * Remove unnecessary anonymous function to map * Introduce an add_breakpoints argument to control adding a breakpoint column * Set add_breakpoint to FALSE to not create a breakpoint column * Document add_breakpoint argument * Merge reports with secondary_reports after filtering leading zeroes * Fix nested ifelse statement * Remove trailing whitespace * Update tests/testthat/test-estimate_secondary.R Co-authored-by: Sebastian Funk <[email protected]> * Replace anonymous function shorthand * Add PR and reviewer Co-authored-by: Sebastian Funk <[email protected]> * Only replace NA with 0 if breakpoint column is present * Only merge by date on secondary_reports Co-authored-by: Sebastian Funk <[email protected]> * Fix test Co-authored-by: Sebastian Funk <[email protected]> * Make sure all the datasets have the same start date * Improve test to compare aspects of fits to original dataset * move filtering up * bring back copying (don't modify input object) * use rstan in tests --------- Co-authored-by: Sebastian Funk <[email protected]>
sbfnk
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…y()` and `estimate_truncation()` (#608) * Add filter_leading_zeros and zero_threshold to estimate_secondary() * Add filter_leading_zeros and zero_threshold to estimate_truncation() * Call create_clean_reported_cases() in estimate_truncation() * Remove breakpoint column created by create_clean_reported_cases() * Add tests for the new arguments * Fix wrong object name * Remove unnecessary anonymous function to map * Introduce an add_breakpoints argument to control adding a breakpoint column * Set add_breakpoint to FALSE to not create a breakpoint column * Document add_breakpoint argument * Merge reports with secondary_reports after filtering leading zeroes * Fix nested ifelse statement * Remove trailing whitespace * Update tests/testthat/test-estimate_secondary.R Co-authored-by: Sebastian Funk <[email protected]> * Replace anonymous function shorthand * Add PR and reviewer Co-authored-by: Sebastian Funk <[email protected]> * Only replace NA with 0 if breakpoint column is present * Only merge by date on secondary_reports Co-authored-by: Sebastian Funk <[email protected]> * Fix test Co-authored-by: Sebastian Funk <[email protected]> * Make sure all the datasets have the same start date * Improve test to compare aspects of fits to original dataset * move filtering up * bring back copying (don't modify input object) * use rstan in tests --------- Co-authored-by: Sebastian Funk <[email protected]>
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Description
This PR closes #605.
Initial submission checklist
devtools::test()anddevtools::check()).devtools::document()).lintr::lint_package()).After the initial Pull Request